Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

ABSTRACT: Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and potential signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin with genetic or induced defects in pigmentation and squamation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial-mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, this comprehensive single-cell transcriptome data from biomedically relevant skin conditions provide a useful resource to accelerate discovery of mechanisms governing skin development.

ORGANISM(S): Danio rerio

PROVIDER: GSE224695 | GEO | 2023/06/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Japanese quail embryonic skin samples

Project description:To understand molecular mechanism of stripe patterning in the embryonic skin of Japanese quail, we compared gene expression profile between black stripe and yelllow stripe by using RNA seq method. Most of differential expression genes were known pigmentation-related genes, but some are unknown role in pigment pattern formation.

2019-02-23 | GSE119008 | GEO

Alterations in Extracellular Matrix Composition during Aging and Photoaging of the Skin

Project description:Human skin is composed of the cell-rich epidermis, the extracellular matrix (ECM) rich dermis, and the hypodermis. Within the dermis, a dense network of ECM proteins provides structural support to the skin and regulates a wide variety of signaling pathways which govern cell proliferation and other critical processes. Both intrinsic aging, which occurs steadily over time, and extrinsic aging (photoaging), which occurs as a result of external insults such as UV radiation, cause alterations to the dermal ECM. In this study, we utilized both quantitative and global proteomics, alongside single harmonic generation (SHG) and two-photon autofluorescence (TPAF) imaging, to assess changes in dermal composition during intrinsic and extrinsic aging. We find that both intrinsic and extrinsic aging result in significant decreases in structural ECM integrity, evidenced by decreasing collagen abundance and increasing fibril fragmentation, and ECM-supporting proteoglycans. Intrinsic aging also produces changes distinct from those produced by photoaging, including reductions in elastic fiber and crosslinking enzyme abundance. In contrast, photoaging is primarily defined by increases in elastic fiber-associated protein and pro-inflammatory proteases. Changes induced by photoaging are evident even in comparisons of young underarm and forearm skin, indicating that photoexposure experienced by an individual’s mid-20s is sufficient for large-scale proteomic alterations and that molecular-level changes due to photoaging are evident well before clinical indications are present. GO term enrichment revealed that both intrinsic aging and photoaging share common features of chronic inflammation.

2020-07-03 | PXD015982 | Pride

Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids

Project description:Patterning and growth are fundamental features of embryonic development that must be tightly coordinated during morphogenesis. While metabolism is known to control cell growth, how it impacts patterning and links to morphogenesis is poorly understood. To understand how metabolism impacts early mesoderm specification during gastrulation, we used in vitro mouse embryonic stem (ES) cell-derived gastruloids, due to ease of metabolic manipulations and high-throughput nature. Gastruloids showed mosaic expression of glucose transporters co-expressing with the mesodermal marker T/Bra. To understand the significance of cellular glucose uptake in development, we used the glucose metabolism inhibitor 2-deoxy-D-glucose (2-DG). 2-DG blocked the expression of T/Bra and abolishes axial elongation in gastruloids. Surprisingly, removing glucose completely from the medium did not phenocopy 2-DG treatment despite a significant decline in glycolytic intermediates occurring under both conditions. As 2-DG can also act as a competitive inhibitor of mannose in protein glycosylation, we added mannose together with 2-DG and found that it could rescue the mesoderm specification. We corroborated these results in vivomouse embryos where supplementing mannose rescued the 2-DG mediated phenotype of mesoderm specification and proximo-distal elongation of the primitive streak. We further showed that blocking production and intracellular recycling of mannose abrogated mesoderm specification. At molecular level, proteomics analysis revealed that mannose reversed glycosylation of the Wnt pathway regulator, Secreted Frizzled Receptor, Frzb, expressed in the primitive streak of the mouse embryo. Our study showed how mannose linked metabolism to glycosylation of a developmental pathway component, crucial in patterning of mesoderm and morphogenesis of gastruloids.

2024-01-12 | MSV000093849 | MassIVE

HEK NICD AP-MS - Notch signaling is a core patterning module for vascular morphogenesis, which co-determines the sprouting behaviour of endothelial cells (ECs)

Project description:Notch signaling is a core patterning module for vascular morphogenesis, which co-determines the sprouting behaviour of endothelial cells (ECs). Tight quantitative and temporal control of Notch activity is essential for vascular development, yet the details of Notch regulation in ECs are incompletely understood. We found that ubiquitin-specific peptidase 10 (USP10) interacted with the NOTCH1 intracellular domain (NICD1) to slow the ubiquitin-dependent turnover of this short-lived form of the activated NOTCH1 receptor. Accordingly, inactivation of USP10 reduced NICD1 abundance and stability, and diminished Notch-induced target gene expression in ECs. In mice, loss of endothelial Usp10 increased vessel sprouting and partially restored the patterning defects caused by ectopic expression of NICD1. Thus, USP10 functions as an NICD1 deubiquitinase, which fine-tunes endothelial Notch responses during angiogenic sprouting.

2019-04-11 | PXD013192 | Pride

Single-cell transcriptomic profile of CD45+ and CD45- cells from dermis and hypodermis of C57BL/6 mice

Project description:In order to explore and compare the transcriptomic profile of leucocytes and stromal cells present in the dermis and hypodermis of C57BL/6 mice, isolated cells from each of these skin layers were subjected to single-cell RNA-sequencing analysis.

2023-09-06 | GSE228018 | GEO

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

Project description:Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

| PRJNA932229 | ENA

Project description:Genetics of wing pigment patterning in rock pigeon

| PRJNA428271 | ENA

Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis [TOMO-seq]

Project description:Integrated in vitro models of human organogenesis are needed to elucidate the multi-systemic events underlying development and disease. We report the generation of human trunk-like structures that model the co-morphogenesis, patterning, and differentiation of the human spine and spinal cord. We identified differentiation conditions for human pluripotent stem cells favoring the formation of an embryo-like extending antero-posterior (AP) axis. Single cell and spatial transcriptomics show that somitic and spinal cord differentiation trajectories organize along this axis and can self-assemble into neural tubes surrounded by somites upon extracellular matrix addition. Morphogenesis is coupled with AP patterning mechanisms which results, at later stages of organogenesis, in in vivo-like arrays of neural subtypes along a neural tube surrounded by spine and muscle progenitors contacted by neuronal projections. This integrated system of trunk development indicates that in vivo-like multi-tissue morphogenesis and topographic organization of terminal cell types can be achieved in human organoids, opening windows for the development of more complex models of organogenesis.

2023-08-31 | GSE215982 | GEO

Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis [scRNA-seq]

2023-08-31 | GSE215981 | GEO

Comprehensive Proteomic Atlas of Skin Biomatrix Scaffolds Reveals a Supportive Microenvironment for Epidermal Development

Project description:Skin is a thin, stratified tissue covering the entire body. It is microscopically defined by layers of epidermal epithelial cells separated from cells in the dermis by a basement membrane (BM), the skin’s extracellular matrix (ECM). The skin’s ECM binds the layers together to form the tissue’s organization and plays important roles in regulation of skin morphogenesis and repair. In this study, skin ECM components have been identified and their interactions with cells characterized using large-scale, quantitative proteomic analysis of skin biomatrix scaffolds, decellularized tissue extracts highly enriched in skin ECM. These were used to quantify structure and function of the skin’s matrix, referred to as the Matrisome, comprised of core ECM components (collagens, proteoglycans and glycoproteins) and of ECM-associated factors, matrix-bound, soluble signals that are key regulators of epidermal development. Analyses on protein-protein interactions of ECMs showed a mechanistic link between hemidesmosome assembly and epidermal homeostasis. This was achieved largely through the integrated network of the hemidesmosome complex and associated proteins mediating anchorage of epidermal stem/progenitors onto skin ECM. These results highlight the power of large-scale proteomics to identify the components and functions of the skin Matrisome regulating tissue homeostasis and ECM remodeling.

2019-07-01 | PXD014454 |

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data